R, RStudio ve RMarkdown ile Tekrarlanabilir Rapor¹

1 Tekrarlanabilir Analiz ve Rapor

1.1 Replication Crisis

https://en.wikipedia.org/wiki/Replication_crisis

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1.2 Replication Crisis

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2 RStudio ile proje oluştur

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3 R Notebook

3.1 R Notebook

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3.2 R Notebook

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3.3 RNotebook vs RMarkdown

https://youtu.be/zNzZ1PfUDNk

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4 R Markdown

4.1 R Markdown: The Definitive Guide

https://bookdown.org/yihui/rmarkdown/

Hem kendi kodları hem de html kodları yazılabilir.

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4.2 R Markdown syntax

https://gist.github.com/MinhasKamal/7fdebb7c424d23149140

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4.3 Remedy

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4.3.1 Remedy

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4.4 Use R Markdown

https://andrewbtran.github.io/NICAR/2018/workflow/docs/02-rmarkdown.html

• Troubleshooting in R Markdown

https://smithcollege-sds.github.io/sds-public/rmarkdown_problems.html

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4.5 Use R Markdown

http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html

• Knitr & R Markdown

https://kbroman.org/knitr_knutshell/pages/overview.html

https://kbroman.org/knitr_knutshell/pages/Rmarkdown.html

https://kbroman.org/knitr_knutshell/pages/markdown.html

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4.6 Use R Markdown

• render markdown via code

inside R

markdown::markdownToHTML('markdown_example.md', 
'markdown_example.html')

command line

R -e "markdown::markdownToHTML('markdown_example.md',
'markdown_example.html')"

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4.7 Use R Markdown

• pandoc Rstudio integration

command line

export PATH=$PATH:/Applications/RStudio.app/Contents/MacOS/pandoc

R -e "rmarkdown::render('markdown_example.md')"

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4.8 Use R Markdown

{r, results='asis'}
 iris %>%
  tibble::as_tibble() %>%
  details::details(summary = 'tibble')

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4.9 Use R Markdown

• Keeping Credentials Secret with Keyrings in R

https://ras44.github.io/blog/2019/01/19/keeping-credentials-secret-with-keyrings-in-r.html

• How to build a website with Blogdown in R

http://www.storybench.org/how-to-build-a-website-with-blogdown-in-r/

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5 Chunk Options

{r global_options, include=FALSE}
knitr::opts_chunk$set(fig.width = 12, fig.height = 8, fig.path = 'Figs/', echo = FALSE, warning = FALSE, message = FALSE, error = FALSE, eval = TRUE, tidy = TRUE, comment = NA)

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6 R Markdown örneği

suppressPackageStartupMessages(library("tidyverse"))
suppressPackageStartupMessages(library("survival"))
suppressPackageStartupMessages(library("finalfit"))

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7 R Markdown örneği

# data("colon_s")
# colon_s
# 
# writexl::write_xlsx(x = colon_s,
#                     path = "data/colon_s.xlsx",
#                     col_names = TRUE,
#                     format_headers = TRUE)

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8 R Markdown örneği

summarytools::what.is(x = lung, 
                      show.all = TRUE, 
                      ignore.size.warn = TRUE)

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9 R Markdown örneği

summarytools descriptives

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10 R Markdown örneği

recode

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11 R Markdown örneği

crosstables

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12 R Markdown örneği

survival

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13 Güncellemeler olunca kodlar çalışacak mı?

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13.1 Paket Kütüphaneleri

• packrat

• renv

https://environments.rstudio.com

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13.2 Docker

• docker

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13.3 Yeni R sürümleri

• RSwitch

https://rud.is/rswitch/

• Using RSwitch

https://rud.is/rswitch/guide/

: scale 30%

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14 Yedeklemeyi nasıl yapacağız

14.1 Save Final Data

{r}
saved data after analysis to `mydata.xlsx`.

save.image(file = here::here("data", "mydata_work_space.RData"))

readr::write_rds(x = mydata, path = here::here("data", "mydata_afteranalysis.rds"))

saveRDS(object = mydata, file = here::here("data", "mydata.rds"))

writexl::write_xlsx(mydata, here::here("data", "mydata.xlsx"))

paste0(rownames(file.info(here::here("data", "mydata.xlsx"))), " : ", file.info(here::here("data", "mydata.xlsx"))$ctime)

14.2 GitHub

{r github push}
CommitMessage <- paste("updated on ", Sys.time(), sep = "")
wd <- getwd()
gitCommand <- paste("cd ", 
                    wd,
                    " \n git add . \n git commit --message '",
                    CommitMessage,
                    "' \n git push origin master \n",
                    sep = ""
                    )
system(command = gitCommand,
       intern = TRUE
)

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14.3 GitHub Yedekleme

CommitMessage <- paste("updated on ", Sys.time(), sep = "")
wd <- getwd()
gitCommand <- paste("cd ", 
                    wd,
                    " \n git add . \n git commit --message '",
                    CommitMessage,
                    "' \n git push origin master \n",
                    sep = ""
                    )

system(command = gitCommand,
       intern = TRUE
)

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15 Her dökümanın sonuna kullandığınız kütüphaneler için atıf yazdırabilirsiniz

{r library citation, echo=TRUE}
citation()

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16 Libraries Used

citation()

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17 Her dökümanın sonuna oturum detaylarınızı yazdırabilirsiniz

{r session info, echo=TRUE}
sessionInfo()

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18 Session Info

sessionInfo()

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19 Sonraki Konular

• RStudio ile GitHub kullanımı
• …

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20 Sunum Linkleri

https://sbalci.github.io/MyRCodesForDataAnalysis/R-Markdown.nb.html https://sbalci.github.io/MyRCodesForDataAnalysis/R-Markdown.html

https://forms.gle/UqGJBiAjB8uLPRon8

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21 Geri Bildirim

• Geri bildirim için tıklayınız: Geri bildirim formu

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22 İletişim

Completed on 2019-09-29.

Serdar Balci, MD, Pathologist
drserdarbalci@gmail.com

https://rpubs.com/sbalci/CV
https://sbalci.github.io/
https://github.com/sbalci
https://twitter.com/serdarbalci

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1. Bu bir derlemedir, mümkün mertebe alıntılara linklerle referans vermeye çalıştım.↩︎